void suggestGene(char *database, char *table, char *prefix)
/* Print out a Javascript list of objects describing genes that start with prefix. */
{
struct dyString *str = newDyString(10000);
dyStringPrintf(str, "[\n");
int exact = cgiOptionalInt("exact", 0);
boolean hasKnownCanonical = sameString(table, "knownCanonical");
initGenbankTableNames(database);
char query[2048];
if(exact)
{
// NOTE that exact is no longer used by the UI as of v271, but there are still some robots
// using it so we still support it.
if(hasKnownCanonical)
sqlSafef(query, sizeof(query),
"select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x "
"where k.transcript = x.kgID and k.transcript = kg.name and x.geneSymbol = '%s' "
"order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix);
else
sqlSafef(query, sizeof(query),
"select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d "
"where r.name2 = '%s' and g.acc = r.name and g.description = d.id "
"order by r.name2, r.chrom, r.txEnd - r.txStart desc",
table, gbCdnaInfoTable, descriptionTable, prefix);
}
else
{
// We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
// Also note that we take advantage of the fact that searches are case-insensitive in mysql.
// Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical;
// 3 POU5F1's in hg19); we return all of them (#5962).
if(hasKnownCanonical)
sqlSafef(query, sizeof(query),
"select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x "
"where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol LIKE '%s%%' "
"order by x.geneSymbol, k.chrom, kg.txStart", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d "
"where r.name2 LIKE '%s%%' and g.acc = r.name and g.description = d.id "
"order by r.name2, r.chrom, r.txStart",
table, gbCdnaInfoTable, descriptionTable, prefix);
}
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
int count = 0;
while ((row = sqlNextRow(sr)) != NULL)
{
// ignore funny chroms (e.g. _hap chroms. See redmine #4257.
if(!strchr(row[1], '_'))
{
// We have some very long descriptions, e.g. 4277 chars for hg38 CLOCK, so truncate:
const int maxDesc = 120;
char *description = row[5];
if (strlen(description) > maxDesc + 4)
strcpy(description + maxDesc, "...");
count++;
dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", "
"\"id\": \"%s:%d-%s\", "
"\"geneSymbol\": \"%s\", "
"\"internalId\": \"%s\"}",
count == 1 ? "" : ",\n", row[0], jsonStringEscape(description),
row[1], atoi(row[2])+1, row[3],
jsonStringEscape(row[0]),
jsonStringEscape(row[4]));
}
}
hFreeConn(&conn);
dyStringPrintf(str, "\n]\n");
puts(dyStringContents(str));
}
void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
hgBotDelay();
cart = theCart;
getDbAndGenome(cart, &database, &genome, oldVars);
initGenbankTableNames(database);
getGenomeSettings();
if (cartVarExists(cart, hggDoKgMethod))
doKgMethod();
else if (cartVarExists(cart, hggDoTxInfoDescription))
doTxInfoDescription();
else
{
struct sqlConnection *conn = NULL;
char *geneName = cartUsualString(cart, hggGene, NULL);
if (isEmpty(geneName))
{
// Silly googlebots.
hUserAbort("Error: the hgg_gene parameter is missing from the cart and the CGI params.");
}
/* if kgProtMap2 table exists, this means we are doing KG III */
if (hTableExists(database, "kgProtMap2")) kgVersion = KG_III;
conn = hAllocConn(database);
curGeneId = findGeneId(conn, geneName);
getGenePosition(conn);
curGenePred = getCurGenePred(conn);
curGeneName = getGeneName(curGeneId, conn);
spConn = hAllocConn(UNIPROT_DB_NAME);
swissProtAcc = getSwissProtAcc(conn, spConn, curGeneId);
if (isRgdGene(conn)) swissProtAcc=getRgdGeneUniProtAcc(curGeneId, conn);
/* Check command variables, and do the ones that
* don't want to put up the hot link bar etc. */
if (cartVarExists(cart, hggDoGetMrnaSeq))
doGetMrnaSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoWikiTrack))
doWikiTrack(conn);
else if (cartVarExists(cart, hggDoGetProteinSeq))
doGetProteinSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoRnaFoldDisplay))
doRnaFoldDisplay(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinSeq))
doOtherProteinSeq(conn, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinAli))
doOtherProteinAli(conn, curGeneId, curGeneName);
else
{
/* Default case - start fancy web page. */
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
struct trackDb *tdb = hTrackDbForTrack(database, genomeSetting("knownGene"));
isGencode = trackDbSettingOn(tdb, "isGencode");
isGencode2 = trackDbSettingOn(tdb, "isGencode2");
cartWebStart(cart, database, "%s Gene %s (%s) Description and Page Index",
genome, curGeneName, isGencode2 ? curGeneId : curAlignId);
webMain(conn, tdb);
cartWebEnd();
}
hFreeConn(&spConn);
hFreeConn(&conn);
}
cartRemovePrefix(cart, hggDoPrefix);
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
char *prefix = cgiOptionalString("prefix");
char *database = cgiOptionalString("db");
initGenbankTableNames(database);
int exact = cgiOptionalInt("exact", 0);
struct sqlConnection *conn;
char query[2048];
char **row;
struct sqlResult *sr;
int count = 0;
boolean hasKnownCanonical;
struct dyString *str = newDyString(10000);
char *table;
pushAbortHandler(htmlVaBadRequestAbort);
if(prefix == NULL || database == NULL)
errAbort("%s", "Missing prefix and/or db CGI parameter");
conn = hAllocConn(database);
table = connGeneSuggestTable(conn);
if(table == NULL)
errAbort("gene autosuggest is not supported for db '%s'", database);
popAbortHandler();
hasKnownCanonical = sameString(table, "knownCanonical");
puts("Content-Type:text/plain");
puts("\n");
dyStringPrintf(str, "[\n");
if(exact)
{
// NOTE that exact is no longer used by the UI as of v271, but there are still some robots using it so we still support it.
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol = '%s' order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d where r.name2 = '%s' and g.acc = r.name "
"and g.description = d.id order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, gbCdnaInfoTable, descriptionTable, prefix);
}
else
{
// We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
// Also note that we take advantage of the fact that searches are case-insensitive in mysql.
// Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical;
// 3 POU5F1's in hg19); we return all of them (#5962).
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k.chrom, kg.txStart", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d where r.name2 LIKE '%s%%' and g.acc = r.name "
"and g.description = d.id order by r.name2, r.chrom, r.txStart", table, gbCdnaInfoTable, descriptionTable, prefix);
}
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
// ignore funny chroms (e.g. _hap chroms. See redmine #4257.
if(!strchr(row[1], '_'))
{
// We have some very long descriptions, e.g. 4277 chars for hg38 CLOCK, so truncate:
const int maxDesc = 120;
char *description = row[5];
if (strlen(description) > maxDesc + 4)
strcpy(description + maxDesc, "...");
count++;
dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", "
"\"id\": \"%s:%d-%s\", "
"\"geneSymbol\": \"%s\", "
"\"internalId\": \"%s\"}",
count == 1 ? "" : ",\n", row[0], jsonStringEscape(description),
row[1], atoi(row[2])+1, row[3],
jsonStringEscape(row[0]),
jsonStringEscape(row[4]));
}
}
dyStringPrintf(str, "\n]\n");
puts(dyStringContents(str));
cgiExitTime("hgSuggest", enteredMainTime);
return 0;
}
